One of the items I sold recently was modified, and I thought a little about this issue. My feeling was that the used market was probably prepared to pay for modifications, especially if they were well known and appreciated. However, the problem is that many modifications tend to be applied to products that are fashionable. So that when the next best thing comes along, these modded units are hard to move.
Take the modded ART DI/O, for example. A few years ago, they were the cats pyjamas. And people like Wayne produced awesome modifications for them. So you could pay a little for the unit, a reasonably small amount for the mods, and you'd have a killer DAC for not much cash. And it's still a killer DAC. But if you try to sell one of these units now I think you'll take a big hit, not because it's modified, but because there's something new that has grabbed everyone's attention (whether it's a Squeezebox, or an Olive, or a DAC 60 or whatever). This risk is there with every hot, new item. BUt I think hot, low-priced, new items are the ones most likely to be modified. I'm sending Wayne my SB2 soon for some mods. In a couple of years, though, I don't imagine it will be worth much on the second hand market.
On the other hand, if you have a well respected, tried and true amplifier that has been around for years, and you can get an upgrade by replacing some caps or whatever, I bet you wouldn't face much downside risk. Some manufacturers have gone out of business, but their products are still resold thanks to the modifiers and upgraders who maintain the value of well-respected, high quality products (e.g. Melos amplifiers).
Chad